Even I'm not sure what to make of this story. You could say it was purely from a Christian perspective and therefore a totally biased parable, but I think there are several ways to take this.
First of all, the basic metaphors should be pretty obvious. I even made it easier to swallow by clearly labelling the religious state of each character.
Second, I apologize for how grumpy the athiest turned out. I couldn't think of another way to portray a man fed up with his companions' stupidities, so he probably appeared more bitter than he should have been. His personality has no relationship to the metaphor of his character; in fact, compared to the athiest, the others are downright bland, so if you want the silver lining there it is.
This brings up an interesting thing I noticed about this story: you, as the reader, get a pretty good idea of what's going on inside the athiest's head when the others do apparently foolish things, but the others are pretty faceless. Maybe that's why the athiest's irritance stood out so much, as in contrast. Anyway, I'll leave it up to you to decide what that means.
Thirdly: Don't ask me what the pebble symbolizes. You could see it as a representative of God and therefore ironic that the athiest doesn't question its supernatural commentary one bit, or you could see it as an excuse to have an outside opinion (which, personally, was the superficial reason). Plus I didn't want to have six men running around the desert; five seemed a much more desirable number.
Fourth-wise, I've had criticism before from people who didn't think I mentioned other religions enough. Since Christians and athiests seem to bicker the most (no joke, from my side of the fence) I just never really gave it much of a thought. Maybe someday a Wiccan or a Hindu will come up with a neat story about debating with athiests and we'll all know the truth. But anyway, back to the point. You'll notice the three religious men in the story are just that: Religious. I'd like to think the structure of the story obscures the exact nature of their religion, asiding nitpicking like "But you said they had 'gods'. I have no gods! I believe in nameless female forces that demand no worship..." and so on. By 'gods' I refer to whatever religious power you believe it (regardless of whether they strike down planes or not). It's just a metaphor, like everything else.
Fifth, and this goes back to my first point, it may seem terribly biased that I ended with the third religious man apprently getting the last laugh. You probably all got the fact that this is supposedly a real city, with real people, and the athiest is probably too bitter and narrow-minded to believe that. But who knows what happened to the man after he went down into the city? Personally, I'd like to think he gets mugged or arrested for poor conduct or something. But maybe he doesn't, and ends up living a happy, peaceful life in a pretty, metaphorical city. Who knows? I'll leave it up to you to decide.
Lastly, the sad tale of the agnostic is actually derived from a lecture I heard by Yann Martel, who wrote "The Life of Pi". I won't explain it but if you know the theme of the book, it should be clear. Anyway, I have no particular harsh feelings towards agnostics, which is appropriate given their neutrality. And it's hard to pick a side when you don't see the appeal of either. But hey, I believe the fence is gonna come down sooner or later. Sorry he came off so idiotic, but how else was that guy supposed to meet his fate without spoiling the symbolism?
Well, there you have it. "Animagess' Top Six Reasons You Shouldn't Flame Her"... I mean, uh, I hope you enjoyed the story and maybe even learned something from it. Nah, you probably just got mad. In fact, if you want to flame, try writing your own version of "Three Men in the Desert" to let off steam. Have all three religious dudes jump into the oasis, only to drown horribly while the athiest lives happily ever after.
I'm not sure how meaningful that will be, but if makes you feel better...
Please review as fairly and considerately as possible.